SBM

Simple example.

Example on how to run the SBM pre-processing using BrainPrep. See user guide for details.

Data

Let’s first get some anatomical data.

from pathlib import Path
from brainprep.datasets import OpenMSDataset
from brainprep.utils import Bunch

datadir = Path("/tmp/brainprep-data")
datadir.mkdir(parents=True, exist_ok=True)
dataset = OpenMSDataset(datadir)
data = Bunch(
    sub01=dataset.fetch(
        subject="01",
        modality="T1w",
        dtype="longitudinal",
    ),
    sub02=dataset.fetch(
        subject="02",
        modality="T1w",
        dtype="longitudinal",
    ),
)
print(data)

[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient01/study1_T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient01/study2_T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient02/study1_T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient02/study2_T1W.nii.gz
Bunch(
  sub01: Bunch(
    description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
    anat1: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz')
    anat2: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz')
  )
  sub02: Bunch(
    description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
    anat1: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz')
    anat2: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz')
  )
)

Analysis

Let’s now perform the preprocessing using BrainPrep. As with many tutorials, we won’t execute the code directly here. However, feel free to set the ‘dryrun’ configuration to False to actually run each step and generate results on disk.

import shutil
from brainprep.workflow import (
    brainprep_sbm,
    brainprep_group_sbm,
    brainprep_longitudinal_sbm,
)
from brainprep.config import Config
from brainprep.reporting import RSTReport

outdir = Path("/tmp/brainprep-sbm")
if outdir.is_dir():
    shutil.rmtree(outdir)
outdir.mkdir(parents=True, exist_ok=True)
with Config(dryrun=True, verbose=True):
    for subject_data in data.values():
        for t1_file in [subject_data.anat1, subject_data.anat2]:
            outputs = brainprep_sbm(
                t1_file=t1_file,
                output_dir=outdir,
                do_lgi=True,
                wm_file=(datadir / "deprecated"),
                keep_intermediate=True,
            )
            (outputs.subject_dir / "stats").mkdir(parents=True, exist_ok=True)
            (outputs.subject_dir / "stats" / "lh.aparc.stats").touch(
                exist_ok=True
            )
    outputs = brainprep_group_sbm(
        output_dir=outdir,
        euler_threshold=-217,
        keep_intermediate=True,
    )
    outputs = brainprep_longitudinal_sbm(
        t1_files=[subject_data.anat1, subject_data.anat2],
        output_dir=outdir,
        keep_intermediate=True,
    )
    for subject_dir in outputs.subject_dirs:
        (subject_dir / "stats").mkdir(parents=True, exist_ok=True)
        (subject_dir / "stats" / "lh.aparc.stats").touch(exist_ok=True)
    outputs = brainprep_group_sbm(
        output_dir=outdir,
        euler_threshold=-217,
        longitudinal=True,
        keep_intermediate=True,
    )

[warn] - BIDS file name does not contain run key: sub-01_ses-study1_T1w.nii.gz
[title] - Subject Level SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_sbm(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01
_ses-study1_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    analysis_type='sbm',
    do_lgi=True,
    wm_file=PosixPath('/tmp/brainprep-data/deprecated'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod':
'T1w', 'run': '15456'}},
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - brainprep interface write-uuid-mapping -input-file
/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1
-entities sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -name uuid_mapping
-full-path False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.write_uuid_mapping(
    input_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub
-01_ses-study1_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
    name='uuid_mapping',
    full_path=False,
)
__________________________________________________________________0.01s, 0.00min
[command] - brainprep interface reconall -t1-file
/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1
-entities sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -t2-file None
-flair-file None -resume False -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.reconall(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01
_ses-study1_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
    t2_file=None,
    flair_file=None,
    resume=False,
)
[command] - recon-all -all -subjid run-15456 -i
/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/scripts/
recon-all.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface localgi -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.localgi(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
)
[command] - recon-all -localGI -subjid run-15456 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface fsaveragesym-surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
)
[command] - brainprep interface xhemireg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.xhemireg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
)
[command] - xhemireg --s run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/xh
emireg.rh.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/xh
emireg.rh.log -command xhemireg -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/xhemi/xhemireg.rh.log'),
    command='xhemireg',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
)
[command] - surfreg --s run-15456 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-15456 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.02s, 0.00min
[command] - brainprep interface fsaveragesym-projection -left-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg -right-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_projection(
    left_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/
ses-study1/run-15456/surf/lh.fsaverage_sym.sphere.reg'),
    right_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
    dryrun=True,
)
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/lh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/surf/rh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study1/run-15456/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.08s, 0.00min
[command] - brainprep interface mgz-to-nii -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mgz_to_nii(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
)
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/aparc+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/aparc+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/aparc.a2009s+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/aparc.a2009s+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.m
gz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.n
ii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/wm.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/wm.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.n
ii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/rawavg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/rawavg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/ribbon.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/ribbon.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/brain.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy1/run-15456/mri/brain.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study1/run-15456/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.nii.gz
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.05s, 0.00min
[command] - brainprep interface freesurfer-tissues -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1
-entities sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -include-cerebellum
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_tissues(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/
ses-study1/workspace_15456'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
    include_cerebellum=False,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/wm
_run-15456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/gm
_run-15456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/cs
f_run-15456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/br
ain_run-15456.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-brainparc -wm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/wm
_run-15456.nii.gz -gm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/gm
_run-15456.nii.gz -csf-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/cs
f_run-15456.nii.gz -brain-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace_15456/br
ain_run-15456.nii.gz -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -entities
sub-01_ses-study1_modality-T1w_mod-T1w_run-15456 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_brainparc(
    wm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/workspace_15456/wm_run-15456.nii.gz'),
    gm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study1/workspace_15456/gm_run-15456.nii.gz'),
    csf_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/
ses-study1/workspace_15456/csf_run-15456.nii.gz'),
    brain_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-0
1/ses-study1/workspace_15456/brain_run-15456.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study1/figures'),
    entities={'sub': '01', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '15456'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/figures/sub-01_ses
-study1_run-15456_brainparc.png
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level SBM done.
__________________________________________________________________0.23s, 0.00min
[warn] - BIDS file name does not contain run key: sub-01_ses-study2_T1w.nii.gz
[title] - Subject Level SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_sbm(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01
_ses-study2_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    analysis_type='sbm',
    do_lgi=True,
    wm_file=PosixPath('/tmp/brainprep-data/deprecated'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod':
'T1w', 'run': '27245'}},
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - brainprep interface write-uuid-mapping -input-file
/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2
-entities sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -name uuid_mapping
-full-path False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.write_uuid_mapping(
    input_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub
-01_ses-study2_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
    name='uuid_mapping',
    full_path=False,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface reconall -t1-file
/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2
-entities sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -t2-file None
-flair-file None -resume False -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.reconall(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01
_ses-study2_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
    t2_file=None,
    flair_file=None,
    resume=False,
)
[command] - recon-all -all -subjid run-27245 -i
/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/scripts/
recon-all.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface localgi -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.localgi(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
)
[command] - recon-all -localGI -subjid run-27245 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface fsaveragesym-surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
)
[command] - brainprep interface xhemireg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.xhemireg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
)
[command] - xhemireg --s run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/xh
emireg.rh.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/xh
emireg.rh.log -command xhemireg -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/xhemi/xhemireg.rh.log'),
    command='xhemireg',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
)
[command] - surfreg --s run-27245 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-27245 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.02s, 0.00min
[command] - brainprep interface fsaveragesym-projection -left-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg -right-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_projection(
    left_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/
ses-study2/run-27245/surf/lh.fsaverage_sym.sphere.reg'),
    right_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
    dryrun=True,
)
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/lh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/surf/rh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/se
s-study2/run-27245/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.08s, 0.00min
[command] - brainprep interface mgz-to-nii -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mgz_to_nii(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
)
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/aparc+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/aparc+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/aparc.a2009s+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/aparc.a2009s+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.m
gz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.n
ii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/wm.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/wm.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.n
ii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/rawavg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/rawavg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/ribbon.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/ribbon.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/brain.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-s
tudy2/run-27245/mri/brain.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01
/ses-study2/run-27245/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.nii.gz
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.05s, 0.00min
[command] - brainprep interface freesurfer-tissues -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2
-entities sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -include-cerebellum
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_tissues(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/
ses-study2/workspace_27245'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
    include_cerebellum=False,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/wm
_run-27245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/gm
_run-27245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/cs
f_run-27245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/br
ain_run-27245.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-brainparc -wm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/wm
_run-27245.nii.gz -gm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/gm
_run-27245.nii.gz -csf-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/cs
f_run-27245.nii.gz -brain-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace_27245/br
ain_run-27245.nii.gz -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -entities
sub-01_ses-study2_modality-T1w_mod-T1w_run-27245 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_brainparc(
    wm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/workspace_27245/wm_run-27245.nii.gz'),
    gm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/s
es-study2/workspace_27245/gm_run-27245.nii.gz'),
    csf_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/
ses-study2/workspace_27245/csf_run-27245.nii.gz'),
    brain_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-0
1/ses-study2/workspace_27245/brain_run-27245.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses
-study2/figures'),
    entities={'sub': '01', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '27245'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/figures/sub-01_ses
-study2_run-27245_brainparc.png
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level SBM done.
__________________________________________________________________0.21s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_ses-study1_T1w.nii.gz
[title] - Subject Level SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_sbm(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02
_ses-study1_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    analysis_type='sbm',
    do_lgi=True,
    wm_file=PosixPath('/tmp/brainprep-data/deprecated'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod':
'T1w', 'run': '38141'}},
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - brainprep interface write-uuid-mapping -input-file
/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1
-entities sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -name uuid_mapping
-full-path False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.write_uuid_mapping(
    input_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub
-02_ses-study1_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
    name='uuid_mapping',
    full_path=False,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface reconall -t1-file
/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1
-entities sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -t2-file None
-flair-file None -resume False -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.reconall(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02
_ses-study1_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
    t2_file=None,
    flair_file=None,
    resume=False,
)
[command] - recon-all -all -subjid run-38141 -i
/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/scripts/
recon-all.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface localgi -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.localgi(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
)
[command] - recon-all -localGI -subjid run-38141 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface fsaveragesym-surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
)
[command] - brainprep interface xhemireg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.xhemireg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
)
[command] - xhemireg --s run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/xh
emireg.rh.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/xh
emireg.rh.log -command xhemireg -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/xhemi/xhemireg.rh.log'),
    command='xhemireg',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
)
[command] - surfreg --s run-38141 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-38141 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.02s, 0.00min
[command] - brainprep interface fsaveragesym-projection -left-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg -right-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_projection(
    left_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/
ses-study1/run-38141/surf/lh.fsaverage_sym.sphere.reg'),
    right_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
    dryrun=True,
)
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/lh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/surf/rh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study1/run-38141/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.08s, 0.00min
[command] - brainprep interface mgz-to-nii -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mgz_to_nii(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
)
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/aparc+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/aparc+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/aparc.a2009s+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/aparc.a2009s+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.m
gz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.n
ii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/wm.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/wm.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.n
ii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/rawavg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/rawavg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/ribbon.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/ribbon.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/brain.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy1/run-38141/mri/brain.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study1/run-38141/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.nii.gz
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.05s, 0.00min
[command] - brainprep interface freesurfer-tissues -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1
-entities sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -include-cerebellum
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_tissues(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/
ses-study1/workspace_38141'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
    include_cerebellum=False,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/wm
_run-38141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/gm
_run-38141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/cs
f_run-38141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/br
ain_run-38141.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-brainparc -wm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/wm
_run-38141.nii.gz -gm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/gm
_run-38141.nii.gz -csf-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/cs
f_run-38141.nii.gz -brain-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace_38141/br
ain_run-38141.nii.gz -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_brainparc(
    wm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/workspace_38141/wm_run-38141.nii.gz'),
    gm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study1/workspace_38141/gm_run-38141.nii.gz'),
    csf_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/
ses-study1/workspace_38141/csf_run-38141.nii.gz'),
    brain_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-0
2/ses-study1/workspace_38141/brain_run-38141.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study1/figures'),
    entities={'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/figures/sub-02_ses
-study1_run-38141_brainparc.png
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level SBM done.
__________________________________________________________________0.21s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_ses-study2_T1w.nii.gz
[title] - Subject Level SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_sbm(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02
_ses-study2_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    analysis_type='sbm',
    do_lgi=True,
    wm_file=PosixPath('/tmp/brainprep-data/deprecated'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod':
'T1w', 'run': '13661'}},
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - brainprep interface write-uuid-mapping -input-file
/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2
-entities sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -name uuid_mapping
-full-path False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.write_uuid_mapping(
    input_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub
-02_ses-study2_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
    name='uuid_mapping',
    full_path=False,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface reconall -t1-file
/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2
-entities sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -t2-file None
-flair-file None -resume False -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.reconall(
    t1_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02
_ses-study2_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
    t2_file=None,
    flair_file=None,
    resume=False,
)
[command] - recon-all -all -subjid run-13661 -i
/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/scripts/
recon-all.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface localgi -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.localgi(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
)
[command] - recon-all -localGI -subjid run-13661 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/scripts/
recon-all.log -command recon-all -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface fsaveragesym-surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
)
[command] - brainprep interface xhemireg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.xhemireg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
)
[command] - xhemireg --s run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/xh
emireg.rh.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/xh
emireg.rh.log -command xhemireg -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/xhemi/xhemireg.rh.log'),
    command='xhemireg',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface surfreg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.surfreg(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
)
[command] - surfreg --s run-13661 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-13661 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.02s, 0.00min
[command] - brainprep interface fsaveragesym-projection -left-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg -right-reg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.fsaveragesym_projection(
    left_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/
ses-study2/run-13661/surf/lh.fsaverage_sym.sphere.reg'),
    right_reg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
    dryrun=True,
)
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.thickness'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.thickness.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.curv'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.curv.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.area'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.area.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.pial_lgi'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.pial_lgi.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/lh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc
[command] - brainprep interface mris-apply-reg -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh -srcreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg -targreg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mris_apply_reg(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.sulc'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/surf/rh.sulc.fsaverage_sym.mgh'),
    srcreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/se
s-study2/run-13661/xhemi/surf/lh.fsaverage_sym.sphere.reg'),
    targreg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/fsaverage_sym/surf/lh.sphere.reg'),
)
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.00s, 0.00min
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh
__________________________________________________________________0.08s, 0.00min
[command] - brainprep interface mgz-to-nii -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mgz_to_nii(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
)
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/aparc+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/aparc+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/aparc.a2009s+aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/aparc.a2009s+aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/aseg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/aseg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.m
gz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.n
ii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/wm.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/wm.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.n
ii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/rawavg.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/rawavg.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/ribbon.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/ribbon.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mri-convert -src-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.mgz -trg-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.nii.gz -reference-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.mri_convert(
    src_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/brain.mgz'),
    trg_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-s
tudy2/run-13661/mri/brain.nii.gz'),
    reference_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02
/ses-study2/run-13661/mri/rawavg.mgz'),
)
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.nii.gz
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.05s, 0.00min
[command] - brainprep interface freesurfer-tissues -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661
-output-dir /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2
-entities sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -include-cerebellum
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_tissues(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/
ses-study2/workspace_13661'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
    include_cerebellum=False,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/wm
_run-13661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/gm
_run-13661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/cs
f_run-13661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/br
ain_run-13661.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-brainparc -wm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/wm
_run-13661.nii.gz -gm-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/gm
_run-13661.nii.gz -csf-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/cs
f_run-13661.nii.gz -brain-mask-file
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace_13661/br
ain_run-13661.nii.gz -output-dir
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -entities
sub-02_ses-study2_modality-T1w_mod-T1w_run-13661 -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_brainparc(
    wm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/workspace_13661/wm_run-13661.nii.gz'),
    gm_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/s
es-study2/workspace_13661/gm_run-13661.nii.gz'),
    csf_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/
ses-study2/workspace_13661/csf_run-13661.nii.gz'),
    brain_mask_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-0
2/ses-study2/workspace_13661/brain_run-13661.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses
-study2/figures'),
    entities={'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/figures/sub-02_ses
-study2_run-13661_brainparc.png
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level SBM done.
__________________________________________________________________0.21s, 0.00min
[title] - Group Level SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_group_sbm(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm'),
    euler_threshold=-217,
    longitudinal=False,
    keep_intermediate=True,
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/workspace
[command] - brainprep interface freesurfer-features-summary -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/workspace -output-dir
/tmp/brainprep-sbm/derivatives/sbm -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_features_summary(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/workspace'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure area
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure volume
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure thickness
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661 sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure thicknessstd
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661 sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure meancurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure gauscurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure foldind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi lh -measure curvind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='lh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure area
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure volume
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure thickness
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661 sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure thicknessstd
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661 sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure meancurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure gauscurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure foldind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -hemi rh -measure curvind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    hemi='rh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-13661
sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface asegstats2table -subjects
sub-02_run-13661,sub-01_run-27245 -session study2 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.asegstats2table(
    subjects=['sub-02_run-13661', 'sub-01_run-27245'],
    session='study2',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study2_stats.csv
--delimiter comma --subjects sub-02_run-13661 sub-01_run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study2_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure area
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure volume
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure thickness
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141 sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure thicknessstd
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141 sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure meancurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure gauscurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure foldind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi lh -measure curvind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='lh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure area
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure volume
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure thickness
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141 sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure thicknessstd
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141 sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure meancurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure gauscurv
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure foldind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -hemi rh -measure curvind
-output-dir /tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    hemi='rh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-02_run-38141
sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface asegstats2table -subjects
sub-02_run-38141,sub-01_run-15456 -session study1 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/morphometry -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.asegstats2table(
    subjects=['sub-02_run-38141', 'sub-01_run-15456'],
    session='study1',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/morphometry'),
)
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study1_stats.csv
--delimiter comma --subjects sub-02_run-38141 sub-01_run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study1_stats.csv
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.24s, 0.00min
[command] - brainprep interface euler-numbers -output-dir
/tmp/brainprep-sbm/derivatives/sbm -euler-threshold -217 -dryrun False -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.euler_numbers(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/quality_check'),
    euler_threshold=-217,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/quality_check/euler_numbers.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-sbm/derivatives/sbm/quality_check/euler_numbers.tsv -col-name
euler_number -output-dir /tmp/brainprep-sbm/derivatives/sbm -bar-coords -217
-dryrun False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_histogram(
    table_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/quality_check/euler
_numbers.tsv'),
    col_name='euler_number',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/figures'),
    bar_coords=[-217],
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/figures/histogram_euler_number.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level SBM done.
__________________________________________________________________0.27s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_ses-study1_T1w.nii.gz
[warn] - BIDS file name does not contain run key: sub-02_ses-study2_T1w.nii.gz
[title] - Longitudinal SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_longitudinal_sbm(
    t1_files=[PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-
02_ses-study1_T1w.nii.gz'),
PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_
T1w.nii.gz')],
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/ses-study1'),
    keep_intermediate=True,
    kwargs={'entities': [{'sub': '02', 'ses': 'study1', 'modality': 'T1w',
'mod': 'T1w', 'run': '38141'}, {'sub': '02', 'ses': 'study2', 'modality': 'T1w',
'mod': 'T1w', 'run': '13661'}]},
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/workspace
[command] - brainprep interface reconall-longitudinal -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/workspace
-output-dir /tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
-entities
sub-02_ses-study1_modality-T1w_mod-T1w_run-38141,sub-02_ses-study2_modality-T1w_
mod-T1w_run-13661 -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.reconall_longitudinal(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/sub
jects/sub-02/workspace'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02'),
    entities=[{'sub': '02', 'ses': 'study1', 'modality': 'T1w', 'mod': 'T1w',
'run': '38141'}, {'sub': '02', 'ses': 'study2', 'modality': 'T1w', 'mod': 'T1w',
'run': '13661'}],
)
[command] - recon-all -base sub-02_template_ses-study1:study2 -tp
sub-02_ses-study1_run-38141 -tp sub-02_ses-study2_run-13661 -all -sd
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
[command] - recon-all -long sub-02_ses-study1_run-38141
sub-02_template_ses-study1:study2 -all -sd
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
[command] - recon-all -long sub-02_ses-study2_run-13661
sub-02_template_ses-study1:study2 -all -sd
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_template_
ses-study1:study2/scripts/recon-all.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
1_run-38141.long.sub-02_template_ses-study1:study2/scripts/recon-all.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
2_run-13661.long.sub-02_template_ses-study1:study2/scripts/recon-all.log
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_template_
ses-study1:study2/scripts/recon-all.log -command recon-all -dryrun False
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects
/sub-02/sub-02_template_ses-study1:study2/scripts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
1_run-38141.long.sub-02_template_ses-study1:study2/scripts/recon-all.log
-command recon-all -dryrun False -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects
/sub-02/sub-02_ses-study1_run-38141.long.sub-02_template_ses-study1:study2/scrip
ts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface freesurfer-command-status -log-file
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
2_run-13661.long.sub-02_template_ses-study1:study2/scripts/recon-all.log
-command recon-all -dryrun False -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_command_status(
    log_file=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects
/sub-02/sub-02_ses-study2_run-13661.long.sub-02_template_ses-study1:study2/scrip
ts/recon-all.log'),
    command='recon-all',
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface movedir -source-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
1_run-38141.long.sub-02_template_ses-study1:study2 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/ses-study1/run-3
8141 -content True -copy False -add-source-basename True -dryrun False -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.movedir(
    source_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/sub-02_ses-study1_run-38141.long.sub-02_template_ses-study1:study2'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/ses-study1/run-38141'),
    content=True,
    copy=False,
    add_source_basename=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/ses-study1/run-3
8141
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface movedir -source-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
2_run-13661.long.sub-02_template_ses-study1:study2 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/ses-study2/run-1
3661 -content True -copy False -add-source-basename True -dryrun False -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.movedir(
    source_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/sub-02_ses-study2_run-13661.long.sub-02_template_ses-study1:study2'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/ses-study2/run-13661'),
    content=True,
    copy=False,
    add_source_basename=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/ses-study2/run-1
3661
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface movedir -source-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_template_
ses-study1:study2 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/template
-content True -copy False -add-source-basename True -dryrun False -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.movedir(
    source_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/sub-02_template_ses-study1:study2'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjec
ts/sub-02/template'),
    content=True,
    copy=False,
    add_source_basename=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/template
__________________________________________________________________0.00s, 0.00min
[title] - Longitudinal SBM done.
__________________________________________________________________0.05s, 0.00min
[title] - Group Level SBM...
________________________________________________________________________________
[call] brainprep.workflow.sbm.brainprep_group_sbm(
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm'),
    euler_threshold=-217,
    longitudinal=True,
    keep_intermediate=True,
)
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/workspace
[command] - brainprep interface freesurfer-features-summary -workspace-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/workspace -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.freesurfer_features_summary(
    workspace_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/wor
kspace'),
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure area -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure volume -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure thickness -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure thicknessstd -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure meancurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure gauscurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure foldind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi lh -measure curvind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='lh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure area -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure volume -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure thickness -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure thicknessstd -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure meancurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure gauscurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure foldind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-13661
-session study2 -hemi rh -measure curvind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    hemi='rh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface asegstats2table -subjects sub-02_run-13661
-session study2 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.asegstats2table(
    subjects=['sub-02_run-13661'],
    session='study2',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study2_stat
s.csv --delimiter comma --subjects sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study2_stat
s.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure area -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure volume -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure thickness -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure thicknessstd -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure meancurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure gauscurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure foldind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi lh -measure curvind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='lh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure area -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='area',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-area_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure volume -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='volume',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-volume_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure thickness -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='thickness',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thickness_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure thicknessstd -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='thicknessstd',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thicknessstd_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure meancurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='meancurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-meancurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure gauscurv -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='gauscurv',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-gauscurv_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure foldind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='foldind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-foldind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface aparcstats2table -subjects sub-02_run-38141
-session study1 -hemi rh -measure curvind -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.aparcstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    hemi='rh',
    measure='curvind',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-curvind_stats.csv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface asegstats2table -subjects sub-02_run-38141
-session study1 -output-dir
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry -verbose True
-dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.asegstats2table(
    subjects=['sub-02_run-38141'],
    session='study1',
    output_dir=PosixPath('/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morpho
metry'),
)
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study1_stat
s.csv --delimiter comma --subjects sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study1_stat
s.csv
__________________________________________________________________0.00s, 0.00min
__________________________________________________________________0.23s, 0.00min
[title] - Group Level SBM done.
__________________________________________________________________0.25s, 0.00min

CLI

Let’s now generate the same analysis using the CLI. The goal here is to translate the workflow calls into explicit shell commands. See user guide for details.

from pprint import pprint

commands = []
commands.append(
    [
        [
            "brainprep", "subject-level-sbm",
            "--t1_file", str(t1_file),
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ] for subject_data in data.values()
          for t1_file in [subject_data.anat1, subject_data.anat2]
    ]
)
commands.append(
    [
        [
            "brainprep", "subject-level-sbm",
            "--t1_file", str(t1_file),
            "--output-dir", str(outdir),
            "--analysis-type", "nextbrain",
            "--keep-intermediate",
        ] for subject_data in data.values()
          for t1_file in [subject_data.anat1, subject_data.anat2]
    ]
)
commands.append(
    [
        [
            "brainprep", "longitudinal-sbm",
            "--t1_files",
            f"{subject_data.anat1},{subject_data.anat2}",
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ] for subject_data in data.values()
    ]
)
commands.append(
    [
        [
            "brainprep", "group-level-sbm",
            "--output-dir", str(outdir),
            "--euler_threshold", "-217",
            "--keep-intermediate",
        ],
        [
            "brainprep", "group-level-sbm",
            "--output-dir", str(outdir),
            "--euler_threshold", "-217",
            "--longitudinal",
            "--keep-intermediate",
        ],
    ]
)
pprint(commands)

[[['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate']],
 [['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate']],
 [['brainprep',
   'longitudinal-sbm',
   '--t1_files',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz,/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'longitudinal-sbm',
   '--t1_files',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz,/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate']],
 [['brainprep',
   'group-level-sbm',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--euler_threshold',
   '-217',
   '--keep-intermediate'],
  ['brainprep',
   'group-level-sbm',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--euler_threshold',
   '-217',
   '--longitudinal',
   '--keep-intermediate']]]

Container

Note that the commands generated by the CLI are not limited to being displayed for reference; they can also be executed directly within the workflow‑dedicated container. By running the commands inside the container, you benefit from a controlled runtime context where all necessary dependencies, libraries, and configuration files are already available. In practice, this means that once the CLI has produced the appropriate instructions, you can simply copy and run them inside the container to achieve the intended results. You can find the BrainPrep images on Docker Hub: Neurospin Docker Hub.

Estimated memory usage: 144 MB